HOMER

Software for motif discovery and next-gen sequencing
analysis

New Hi-C analysis routines in HOMER

Many of HOMER's Hi-C analysis tools have been
upgraded and changed. Most of the tools below still
work, but some of the default behavior has changed.
In general we recommend you follow the new Hi-C workflows
here.

Analyzing Hi-C genome-wide interaction data

HOMER contains several programs and analysis routines to
facilitate the analysis of Hi-C data. Hi-C couples chromosome
conformation capture (3C) with deep sequencing to
reveal regions of genomic DNA that are in close spatial
proximity in the nucleus. Hi-C has emerged as a
powerful technique to understand how the genome is packaged
in cells to control gene expression. Unlike ChIP-PET,
5C, or 4C, Hi-C is unbiased. While HOMER can be
jury-rigged to gleam information from other 3C-sequencing
based methods, it has been specifically tailored Hi-C
analysis.

Several tools for analyzing Hi-C data with HOMER have been
upgraded. However, the tools described below are still
available within the HOMER software. If you want to learn
more about the newer tools, a description of the newer
version of HOMER's Hi-C analysis routines can be found here.

Specialized Hi-C programs in HOMER

HOMER has several specialized programs for Hi-C
analysis. Each is covered in the tutorials below:

makeTagDirectory - special paired-end
operations for making HOMER-style tag directories and
filtering options for Hi-C
analyzeHiC - primary analysis program - generates
interaction matrices, normalization, identification of
significant interactions, clustering of domains, generates
Circos plots (most of the following programs use this one
internally)runHiCpca.pl -
automated PCA analysis on Hi-C data to identify
"compartments"getHiCcorrDiff.pl
- calculates the difference in correlation profiles
between two Hi-C experimentsfindHiCCompartments.pl
- find continuous or differential regions from
PCA/corrDiff results that describe what compartment
regions of DNA belong to (name changed - was called getDomains.pl)
findHiCInteractionsByChr.pl - helps automate the
finding of high-resolution intra-chromosomal interactionsannotateInteractions.pl -
program for re-analysis of significant interactions, such
as relating them to ChIP-Seq peaks
SIMA.pl - Novel tool to boost sensitivity by pooling
features together when performing interaction calculations

3rd Party Software

The following 3rd Party [Free] Software
is used by HOMER for visualizing Hi-C results. They
are required for specific functions (i.e. if you don't
care about PCA, don't worry about installing R). Most
are straightforward to install: